I've generated different 'envelopes' from SAXS data that are different deletion constructions of the same protein, ie I have data from the full length protein and 2 constructions that are missing different parts of the aa sequence. All 3 constructions have at least 1 part of the sequence (1 domain) in common.
So I was wondering, is there a way to align these 3 envelopes so I could identify the common domain (other than manually trying to fit them together)?

I don't think there's any way you can do that with envelopes that you have already calculated. However, you can calculate new pre-aligned dummy atom models using MONSA. For the deletion constructs, just tell the program that the deleted domain is "contrast-matched" out.